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dnarnaresearch.bsky.social
@dnarnaresearch.bsky.social
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dnarnaresearch.bsky.social
Towards accurate, reference-free differential expression: A comprehensive evaluation of long-read de novo transcriptome assembly
doi.org/10.1101/2025...

High Quality de Novo Transcriptome Assembly of Croton tiglium
doi.org/10.3389/fmol...
Towards accurate, reference-free differential expression: A comprehensive evaluation of long-read de novo transcriptome assembly
Long-read RNA sequencing has significantly advanced transcriptomics by enabling the full length of transcripts to be assessed. However, current analysis methods often depend on a high-quality referenc...
doi.org
December 7, 2025 at 6:24 AM
dnarnaresearch.bsky.social
Rapid adaptation follows experimental assisted gene flow in subset of annual monkeyflower populations
doi.org/10.64898/202...

Genetic factors explaining anthocyanin pigmentation differences
doi.org/10.1101/2023...
doi.org
December 5, 2025 at 9:09 PM
Reposted
thorstenlangner.bsky.social
Great news for new plant breeding technologies in Europe! 🥳 EU reaches preliminary deal on gene editing!
www.consilium.europa.eu/en/policies/...
New genomic techniques for plant breeding
New genomic techniques can increase food security and mitigate climate change effects. EU rules aim to regulate these plant breeding methods.
www.consilium.europa.eu
December 4, 2025 at 7:41 PM
Reposted
manu-lera.bsky.social
#OpenCloning is a an Open Source alternative to SnapGene/Benchling that supports automation and integration with other software

✅ Free
🔓 Open Source
🧬 More cloning methods than SnapGene
🤖 Can be automated with python
👨‍🔬 Built by a researcher — for researchers!

👉 Check it out at opencloning.org
A cloning strategy as depicted in the OpenCloning website
November 24, 2025 at 4:57 PM
Reposted
bpucker.bsky.social
I had the honor of giving my inaugural lecture at the University of Bonn: “Big Data-Driven Discoveries in Specialized Plant Metabolism.” Grateful to everyone who attended and for the inspiring discussions afterward!
www.pbb.uni-bonn.de
#PlantScience #BigData #AcademicLife @puckerlab.bsky.social
Title slide of inaugural lecture: "Big Data-Driven Discoveries in Specialized Plant Metabolism"
December 4, 2025 at 8:31 PM
dnarnaresearch.bsky.social
A dual DNA/RNA-binding factor regulates co-transcriptional splicing through target RNA interaction and modulates splicing factor dynamics
doi.org/10.1101/2024...

Animal, fungi, and plant genome sequences harbour different non-canonical splice sites
doi.org/10.1101/616565
A dual DNA/RNA-binding factor regulates co-transcriptional splicing through target RNA interaction and modulates splicing factor dynamics
How RNA splicing events are targeted to the correct genomic locations in specific cellular contexts to generate context-specific transcript diversity remains very poorly understood. We show that a fun...
doi.org
December 4, 2025 at 1:35 AM
Reposted
plantevolution.bsky.social
...nothing against the work, but I wonder how useful such information is as long as the alternatives are not considered. Plus, how does it stack up against natural compounds that we come in touch with every day?
December 3, 2025 at 9:15 AM
dnarnaresearch.bsky.social
Mut-BPE: A Modified BPE Strategy Improves Variant Effect Prediction
doi.org/10.1101/2025...

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718
Mut-BPE: A Modified BPE Strategy Improves Variant Effect Prediction
Byte Pair Encoding (BPE) is widely used in genome foundation models for its ability to compress long DNA sequences into fewer tokens. However, its variable-length tokens often span multiple nucleotide...
doi.org
December 3, 2025 at 7:15 AM
dnarnaresearch.bsky.social
Caris-ComBat-seq: Directionally Harmonizing Large-Scale RNA-seq Datasets
doi.org/10.1101/2025...

The reuse of public datasets in the life sciences: potential risks and rewards
doi.org/10.7717/peer...
Caris-ComBat-seq: Directionally Harmonizing Large-Scale RNA-seq Datasets
Background. Bulk RNA sequencing (RNA-seq) is an essential research and clinical diagnostics tool capable of uncovering biological insights across experimental conditions, sample types and diseases at ...
doi.org
December 2, 2025 at 5:49 AM
dnarnaresearch.bsky.social
charisma: An R package to perform reproducible color characterization of digital images for biological studies
doi.org/10.1101/2025...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
charisma: An R package to perform reproducible color characterization of digital images for biological studies
Advances in digital imaging and software tools have provided increasingly accessible datasets and methods for analyzing color evolution. Despite the variety of computational packages available, most r...
doi.org
December 2, 2025 at 5:48 AM
dnarnaresearch.bsky.social
NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing
doi.org/10.1101/2025...

Genome sequence of the blue flowering Centaurea cyanus
doi.org/10.1101/2025...
NanoporeDB: A Structural Resource Of Multimeric Protein Nanopores In Single-Molecule Sensing
Protein nanopores are essential molecular gateways in biology and have inspired transformative technologies in biosensing and single-molecule sequencing. While this technology has transformed genomics...
doi.org
November 30, 2025 at 10:34 AM
Reposted
guijacquemet.bsky.social
Your periodic reminder that science is not done by a few selected "stars scientists". Science is done by hundred of thousands. Siloed money mean a few flashy discoveries and a lot of waste. Want to change things? Make funding accessible and stop funding calls with less than 2% success rate.
katherinestiles.org Katherine Stiles @katherinestiles.org · 9d
· #AcademicSky ·
The European Research Council is launching €7m Plus Grants for ambitious, long‑term research — open to researchers at any career stage but limited to about 30 awards; current ERC grantees and applicants are ineligible, reports @clanicholson.bsky.social.
ERC’s new €7m Plus Grants open to researchers at any career stage - Research Professional News
European Research Council president describes scheme as part attempt to lure US talent
www.researchprofessionalnews.com
November 29, 2025 at 10:53 AM
Reposted
jbyoder.org
Orchids are famous for specialized flowers that create species isolation by manipulating pollinators— but these ones don't have specialized pollinator relationships. Instead, they're isolated by pollen incompatibilities. 🌿

buff.ly/Ypb77Ir
Flowers of the orchid Anacamptis papilionacea, pink and butterfly-shaped with wide darker wings; photo by Hans Hillewaert via Wikimedia Commons Flowers of the orchid Anacamptis pyramidalis, lighter pink and with big lip-like labellums; photo by Ramin Nakisa via Wikimedia Commons Flowers of the orchid Anacamptis morio hampe, purple with long nectar spurs and big lip-like labellums; photo by Didier Desouens, via Wikimedia Commons
November 28, 2025 at 3:12 PM
Reposted
vegplotter.bsky.social
French Marigolds are a game-changer for whitefly control! 🌼🚫They release Limonene, a strong scent that acts as a natural repellent. The aroma confuses airborne pests & "jams" their navigation, stopping them from landing on your prized veggies. 🍅
Nature’s very own forcefield! 🛡️ #OrganicGardening
Yellow French Marigolds with tomato plants in the background
November 28, 2025 at 11:49 PM
Reposted
vegplotter.bsky.social
🎉Cyber Monday Alert! 🎉

Missed Black Friday?

Don't worry! Grab 20% OFF all VegPlotter subscriptions on Monday, Dec 1st, 2025!

Keep your eyes peeled on Monday for the promo code! 🥕💻
person using computer and phone with vegplotter on the screen with a cup of coffee to the side on a desk
November 29, 2025 at 12:01 AM
Reposted
agristok.bsky.social
5 Fully Funded PhD Positions in Molecular Plant Science at International Max Planck Research School (IMPRS), Germany

Explore how to join the fully funded IMPRS Molecular Plant Science PhD program at the Max Planck Institute and University of Potsdam. Learn about benefits, application requirements,…
5 Fully Funded PhD Positions in Molecular Plant Science at International Max Planck Research School (IMPRS), Germany
Explore how to join the fully funded IMPRS Molecular Plant Science PhD program at the Max Planck Institute and University of Potsdam. Learn about benefits, application requirements, training structure, and why international students worldwide choose this top-tier research environment.
agristok.net
November 29, 2025 at 12:23 AM
dnarnaresearch.bsky.social
Gene duplication drove functional divergence of two effectors in the maize anthracnose pathogen
doi.org/10.1101/2025...

DupyliCate - mining, classifying, and characterizing gene duplications
doi.org/10.1101/2025...
Gene duplication drove functional divergence of two effectors in the maize anthracnose pathogen
Colletotrichum species rank among the most important fungal pathogens, threatening food security by infecting nearly all major crops worldwide. Colletotrichum graminicola, the causal agent of maize an...
doi.org
November 29, 2025 at 6:14 AM
Reposted
jbyoder.org
Really good, evenhanded treatment of this issue, starting from the problem that we’ve conflated a bunch of generative algorithms with ML methods used for actual new analysis under the “AI” brand
November 28, 2025 at 5:53 PM
dnarnaresearch.bsky.social
Haplotype-resolved diploid genome inference on pangenome graphs
doi.org/10.1101/2025...

The haplotype-resolved assembly of COL40 (Manihot esculenta)
doi.org/10.1101/2024...
Haplotype-resolved diploid genome inference on pangenome graphs
Genotyping is the task of identifying the genetic variants present in a sample from sequencing data, and it is a fundamental problem in computational biology. Existing genotyping approaches typically ...
doi.org
November 28, 2025 at 9:33 PM
dnarnaresearch.bsky.social
Eduomics: a Nextflow pipeline to simulate -omics data for education
doi.org/10.1101/2025...

Integrating Molecular Biology and Bioinformatics Education
doi.org/10.1515/jib-...
Eduomics: a Nextflow pipeline to simulate -omics data for education
Moving past learning just algorithms and code is a key challenge of bioinformatics education: the ideal goal is for students to acquire higher-order knowledge such as the ability to solve biological p...
doi.org
November 28, 2025 at 9:31 PM
dnarnaresearch.bsky.social
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
doi.org/10.1101/2025...

KIPEs3: Automatic annotation of biosynthesis pathways
doi.org/10.1101/2022...
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing
The FASTQ file format is the lingua franca of primary data distribution and processing across most of bioinformatics. Over time, the compression, storage, transmission, and decompression of gzip compr...
doi.org
November 28, 2025 at 9:23 PM
Reposted
bpucker.bsky.social
Corinna and I were awarded the “FAIR Software Award Lower Saxony 2025” on Monday at TU Braunschweig!

We are thrilled that our bHLH_annotator tool convinced the jury.

Check it out here: doi.org/10.1186/s128...

#OpenScience #FAIR #Python @puckerlab.bsky.social
Pictures of the award ceremony at TU Braunschweig. Some pictures were taken by Henry Fiebig.
November 28, 2025 at 5:41 AM
Reposted
frwildflowers.bsky.social
Penstemon angustifolius var. angustifolius
(Broadbeard Penstemon) blooming in Fremont Canyon #nativeplants

#FallBackFlowers #FallBack to May 27 🌿
Cheerful blue penstemon flowers
November 27, 2025 at 3:34 PM
Reposted
ashs-hort.bsky.social
Happy Thanksgiving from all of us at ASHS!

https://ashs.org/
November 27, 2025 at 12:00 PM
Reposted
davidcayjohnston.bsky.social
The latest evidence that America is becoming a land of idiots:
November 27, 2025 at 7:18 AM